I think you already have a built turbo G right? I'd say go w/ what you know and turbo the FX50. Custom turbo is relatively easy, you can put it almost anywhere, just need piping and oil lines. With a custom SC, you'd have to have custom brackets built that are in perfect alignment, etc. Plus the powerband of the turbo is much better; more low end torque and you don't have to wait until redline to hit full boost.
I had a Maxima back in the day. Put a Stillen SC on it (Vortech); even though it was a kit, that thing was never in alignment and it shredded belts about as frequently as I needed to change the oil. No matter how many shims/spacers we used to align the thing, it was never right. Eventually I got tired of it and custom built a turbo set up since there weren't any kits I liked. It was surprisingly much easier than I thought it was going to be. It's just pipes, as long as you have the space to put the turbo, it's pretty simple (only took about 3 days of cutting/fitting/mockups before the setup was ready to be welded). I'd say the hardest parts for you are likely going to be fuel delivery and engine management which would have been issues w/ the SC anyways.